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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Rhodospirillum centenum (strain ATCC 51521 / SW)
Status
Reviewed-Annotation score: -Protein inferred from homologyi

Functioni

Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan.UniRule annotation

Catalytic activityi

LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate.UniRule annotation

Pathwayi: L-lysine biosynthesis via DAP pathway

This protein is involved in step 1 of the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Diaminopimelate epimerase (dapF)
This subpathway is part of the pathway L-lysine biosynthesis via DAP pathway, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate, the pathway L-lysine biosynthesis via DAP pathway and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei13SubstrateUniRule annotation1
Binding sitei46SubstrateUniRule annotation1
Binding sitei66SubstrateUniRule annotation1
Active sitei75Proton donorUniRule annotation1
Binding sitei156SubstrateUniRule annotation1
Sitei158Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Binding sitei189SubstrateUniRule annotation1
Sitei207Could be important to modulate the pK values of the two catalytic cysteine residuesUniRule annotation1
Active sitei216Proton acceptorUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase
Biological processAmino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciRCEN414684:G1G8I-2110-MONOMER
UniPathwayiUPA00034; UER00025

Names & Taxonomyi

Protein namesi
Recommended name:
Diaminopimelate epimeraseUniRule annotation (EC:5.1.1.7UniRule annotation)
Short name:
DAP epimeraseUniRule annotation
Alternative name(s):
PLP-independent amino acid racemaseUniRule annotation
Gene namesi
Name:dapFUniRule annotation
Ordered Locus Names:RC1_2197
OrganismiRhodospirillum centenum (strain ATCC 51521 / SW)
Taxonomic identifieri414684 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodospirillalesRhodospirillaceaeRhodospirillum
Proteomesi
  • UP000001591 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10001244291 – 291Diaminopimelate epimeraseAdd BLAST291

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi414684.RC1_2197

Structurei

3D structure databases

ProteinModelPortaliB6IP82
SMRiB6IP82
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni76 – 77Substrate bindingUniRule annotation2
Regioni207 – 208Substrate bindingUniRule annotation2
Regioni217 – 218Substrate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105E4Z Bacteria
COG0253 LUCA
HOGENOMiHOG000220466
KOiK01778
OMAiSMCGNGG
OrthoDBiPOG091H01QC

Family and domain databases

HAMAPiMF_00197 DAP_epimerase, 1 hit
InterProiView protein in InterPro
IPR018510 DAP_epimerase_AS
IPR001653 DAP_epimerase_DapF
PANTHERiPTHR31689 PTHR31689, 1 hit
PfamiView protein in Pfam
PF01678 DAP_epimerase, 2 hits
TIGRFAMsiTIGR00652 DapF, 1 hit
PROSITEiView protein in PROSITE
PS01326 DAP_EPIMERASE, 1 hit

Sequencei

Sequence statusi: Complete.

B6IP82-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVRRFLKMHG LGNDFVVLDA RRDPLPLTTA AARAIADRHT GVGCDQIVLL
60 70 80 90 100
EPPRHPAADL FMRILNPDGS ESGACGNATR CVASLVADGS GRAEVTVETA
110 120 130 140 150
TGLLRCRLRA DGSVTVDMGP ARLDWTQIPL AAAHDTLRVP AGAGPLQDAC
160 170 180 190 200
CVGMGNPHAV FFVDDAEAVD LATLGPVLEH HSLFPQRCNI EVAQVLAPDH
210 220 230 240 250
IRMRVWERGA GITRACGSGS CATLVAAARR GLTGRAAWIE LDGGRLWIEW
260 270 280 290
HGDGHVLMTG PVATAFTGEL SETLLPGSLP SETPLPETVP A
Length:291
Mass (Da):30,704
Last modified:December 16, 2008 - v1
Checksum:i0B546D7062B5895C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000613 Genomic DNA Translation: ACI99584.1
RefSeqiWP_012567369.1, NC_011420.2

Genome annotation databases

EnsemblBacteriaiACI99584; ACI99584; RC1_2197
KEGGirce:RC1_2197

Similar proteinsi

Entry informationi

Entry nameiDAPF_RHOCS
AccessioniPrimary (citable) accession number: B6IP82
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: December 16, 2008
Last modified: March 28, 2018
This is version 56 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome
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Main funding by: National Institutes of Health